Microfluidic devices and methods have been developed and used for a variety of analytical applications, including high throughput screening for drug discovery, gene expression analysis, and disease diagnosis. In the recent years, there has been a great interest in the use of microfluidic systems for synthetic biology applications. Accordingly, there is a need to develop microfluidic devices and methods for the synthesis of polynucleotides and reduce the cost, processing time and limit the use of reagents.